Updated pangolin v4.3.1 pangolin-data 1.28 scorpio v0.3.19 constellations v0.1.12

Author: fredericlemoine

pangolin/v4.3.1-v1.28-v0.3.19-v0.1.12/Dockerfile

@@ -0,0 +1,44 @@
+# Largely inspired from
+#  https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
+
+FROM continuumio/miniconda3:23.5.2-0-alpine
+LABEL version="4.3.1" \
+      description="Docker image for Pangolin"
+
+ENV VERSION "v4.3.1"
+ENV DATAVERSION "v1.28"
+ENV SCORPIOVERSION "v0.3.19"
+ENV CONSTELLATIONVERSION "v0.1.12"
+
+# Install git for pangolin
+RUN apk update \
+    && apk add git bash libarchive \
+    && pip install --upgrade pip \
+    && pip uninstall --yes pyOpenSSL \
+    && pip install --upgrade cryptography \
+    && pip install pyOpenSSL \
+    && conda update conda \
+    && conda update --all \
+    && conda install mamba -c conda-forge
+
+COPY pangolin.patch /
+
+RUN cd / \
+    && git clone https://github.com/cov-lineages/pangolin.git \
+    && cd pangolin \
+    && git checkout $VERSION \
+    && git apply /pangolin.patch \
+    && cd .. \
+    && sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
+    && sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
+    && sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
+    && sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
+    && sed -i s/pip=.*/pip/ /pangolin/environment.yml \
+    && mamba env update  --quiet -f /pangolin/environment.yml && conda clean -a \
+    && cd /pangolin \
+    && pip install . && rm -rf /root/.cache/pip \
+    && pangolin --version &> /pangolin-version.txt
+    
+WORKDIR /tmp/
+
+ENTRYPOINT ["pangolin"]

pangolin/v4.3.1-v1.28-v0.3.19-v0.1.12/pangolin.patch

@@ -0,0 +1,12 @@
+diff --git a/pangolin/scripts/usher.smk b/pangolin/scripts/usher.smk
+index 3adffc7..3ba0938 100644
+--- a/pangolin/scripts/usher.smk
++++ b/pangolin/scripts/usher.smk
+@@ -106,6 +106,7 @@ rule usher_inference:
+                 echo ""
+             fi
+             cat {input.fasta:q} >> {params.ref_fa:q}
++            sed -i 's/^ *//' {params.ref_fa:q}
+             faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
+             $usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
+         else